Merge pull request #12 from PetterHopp/main

OKplan v0.6.1

.gitignore

@@ -1,7 +1,41 @@
-.Rproj.user
+# History files
 .Rhistory
+.Rapp.history
+
+# Session Data files
 .RData
+
+# User-specific files
 .Ruserdata
-*.Rproj
-*.Rcheck
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# R Environment Variables
+.Renviron
+
 inst/doc

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: OKplan
 Title: Tools to facilitate the Planning of the annual Surveillance Programmes
-Version: 0.6.0
-Date: 2023-05-30
+Version: 0.6.1
+Date: 2023-10-09
 Authors@R: 
   c(person(given = "Petter",
            family = "Hopp",
@@ -35,6 +35,7 @@ Imports:
     OKcheck
 Suggests:
     covr,
+    desc,
     devtools,
     testthat,
     usethis,

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2020, Norwegian Veterinary Institute
+Copyright (c) 2020 - 2023 Norwegian Veterinary Institute
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

NEWS

@@ -1,3 +1,18 @@
+OKplan 0.6.1 - (2023-10-09)
+----------------------------------------
+
+Bug fixes:
+
+- the argument `year` in `get_tested_herds` now accepts more than one year as input. 
+
+- The argument column can now be passed to append_sum_line.
+
+
+Other changes:
+
+- Updated help section in README
+
+
 OKplan 0.6.0 - (2023-05-30)
 ----------------------------------------
 

OKplan.Rproj

@@ -0,0 +1,17 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source

R/adjust_samples_to_budget.R

@@ -118,10 +118,10 @@ adjust_samples_to_budget <- function(data,
 
   difference <- difference %>%
     dplyr::mutate(original_order = 1:dplyr::n()) %>%
-    dplyr::arrange(dplyr::across(c(group, sample_to_adjust))) %>%
+    dplyr::arrange(dplyr::across(dplyr::all_of(c(group, sample_to_adjust)))) %>%
     dplyr::group_by(dplyr::across(dplyr::all_of(group))) %>%
     dplyr::mutate(total_estimated = sum(dplyr::across(dplyr::all_of(sample_to_adjust)), na.rm = TRUE)) %>%
-    dplyr::mutate(included = dplyr::case_when(dplyr::across(sample_to_adjust) > 0 ~ 1,
+    dplyr::mutate(included = dplyr::case_when(dplyr::across(dplyr::all_of(sample_to_adjust)) > 0 ~ 1,
                                               TRUE ~ 0)) %>%
     dplyr::mutate(n_units = sum(.data$included, na.rm = TRUE)) %>%
     dplyr::mutate(difference = .data$total_estimated - as.numeric(.data$budget)) %>%

R/get_tested_herds.R

@@ -62,7 +62,7 @@ get_tested_herds <- function(eos_table,
   checkmate::assert_integerish(year,
                                lower = 1995, upper = (as.numeric(format(Sys.Date(), "%Y"))),
                                any.missing = FALSE, all.missing = FALSE,
-                               len = 1,
+                               min.len = 1,
                                add = checks)
   checkmate::assert_character(species, min.len = 1, null.ok = TRUE, add = checks)
   checkmate::assert_character(production, min.len = 1, null.ok = TRUE, add = checks)

R/write_ok_selection_list.R

@@ -41,6 +41,13 @@
 #'
 #' All vectors must have the same order and the same length.
 #'
+#' When \code{\link{calculate_sum}} is TRUE, a line with the sum will be appended.
+#'    The default is to calculate the sum of the column "ant_prover". If the sum
+#'    should be calculated for one or more other columns, you may give thecolumn
+#'    names as input to the argument \code{column} that will be passed to
+#'    \code{\link{append_sum_line}}. The sum will only be appended for columns
+#'    that exist in the data.
+#'
 #' When more than one worksheet should be added to a single workbook,
 #'     use \code{add_worksheet = FALSE} for the first worksheet and
 #'     \code{add_worksheet = TRUE} for the consecutive worksheet(s).
@@ -70,6 +77,7 @@
 #' @param add_worksheet [\code{logical(1)}]\cr
 #'     Should a worksheet be added to an existing workbook? Defaults to
 #'     \code{FALSE}.
+#' @param \dots Other arguments to be passed to \code{\link{append_sum_line}}.
 #' @export
 #'
 write_ok_selection_list <- function(data,
@@ -81,11 +89,13 @@ write_ok_selection_list <- function(data,
                                     footnote = NULL,
                                     footnote_heights = NULL,
                                     dbsource,
-                                    add_worksheet = FALSE) {
+                                    add_worksheet = FALSE,
+                                    ...) {
 
   # PREPARE ARGUMENTS BEFORE ARGUMENT CHECKING ----
   # Remove trailing backslash or slash before testing path
   filepath <- sub("\\\\{1,2}$|/{1,2}$", "", filepath)
+  dots <- list(...)
 
   # ARGUMENT CHECKING ----
   # Object to store check-results
@@ -179,7 +189,13 @@ write_ok_selection_list <- function(data,
   # INCLUDE EXTRA INFORMATION ----
   # Append sum
   if (isTRUE(calculate_sum)) {
-    okdata <- append_sum_line(data = okdata, column = c("ant_prover"), position = "left")
+    if ("column" %in% names(dots)) {
+      column <- dots$column
+      } else {column <- "ant_prover"}
+    column <- intersect(column, colnames(data))
+    if (length(column) > 0) {
+      okdata <- append_sum_line(data = okdata, column = column, position = "left")
+    }
   }
 
   # Append date generated

README.Rmd

@@ -6,21 +6,27 @@ output:
 
 params:
   NVIpkg: "OKplan"
+  pkg_path: !r  usethis::proj_path()
   first_copyright_year: "2021"
 ---
 
 ```{r, include = FALSE}
 NVIpkg <- params$NVIpkg
-# NVIpkg <- stringi::stri_extract_last_words(usethis::proj_path())
 NVIpkg_inline <- paste0("`", NVIpkg, "`")
+pkg_path <- params$pkg_path
+
+logo_path <- ""
+if (file.exists(paste0("./man/figures/", NVIpkg, "_logo.png"))) {
+  logo_path <- paste0(' <img src="man/figures/', NVIpkg, '_logo.png" align="right" height="138" />')
+}
 
 knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>"
 )
 ```
 
-`r paste0(NVIpkg, ": ", desc::desc_get_field(key = "Title"))`
+`r paste0(NVIpkg, ": ", desc::desc_get_field(key = "Title"), logo_path)`  
 ================
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->

README.md

@@ -1,4 +1,4 @@
-# OKplan: Tools to facilitate the Planning of the annual Surveillance Programmes
+# OKplan: Tools to facilitate the Planning of the annual Surveillance Programmes <img src="man/figures/OKplan_logo.png" align="right" height="138" />
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
@@ -55,17 +55,34 @@ The `OKplan` package needs to be attached.
 surveillance programmes. The main focus is tools for generating
 standardized lists for NFSA.
 
+#### Further documentation
+
+##### Help
+
 The full list of all available functions and datasets can be accessed by
 typing
 
     help(package = "OKplan")
 
-Please check the NEWS for information on new features, bug fixes and
-other changes.
+##### Vignettes
+
+Consult the vignettes for task-oriented help.
+
+    vignette(package = "OKplan")
+
+Vignettes in package `OKplan`:
+
+-   Contribute to OKplan (html)
+
+##### NEWS
+
+Please check the
+[NEWS](https://github.com/NorwegianVeterinaryInstitute/OKplan/blob/main/NEWS)
+for information on new features, bug fixes and other changes.
 
 ## Copyright and license
 
-Copyright (c) 2021 - 2022 Norwegian Veterinary Institute.  
+Copyright (c) 2021 - 2023 Norwegian Veterinary Institute.  
 Licensed under the BSD\_3\_clause License. See
 [License](https://github.com/NorwegianVeterinaryInstitute/OKplan/blob/main/LICENSE)
 for details.

notes/develop.R

@@ -16,12 +16,19 @@ pkg <- stringi::stri_extract_last_words(pkg_path)
 
 
 # CREATE PACKAGE SKELETON ----
-# create_NVIpkg_skeleton(license_keyword = "CC BY 4.0")
+# create_NVIpkg_skeleton(license_keyword = "BSD_3_clause") # BSD_3_clause # CC BY 4.0
 
 # INCREASE PACKAGE VERSION IN DESCRIPTION AND NEWS ----
 # NVIpackager::increase_NVIpkg_version(pkg = pkg,
 #                                   pkg_path = pkg_path,
-#                                   type = "develop")
+#                                   type = "develop",
+#                                   document = FALSE)
+
+# UPDATE LICENSE
+# NVIpackager::update_license(pkg = pkg,
+#                             pkg_path = pkg_path,
+#                             copyright_owner = "Norwegian Veterinary Institute")
+
 
 # DOCUMENTATION AND STYLING ----
 # update_logo should be run if a logo has been created (or updated). Thereafter run "document_NVIpkg" with "readme = TRUE".
@@ -36,6 +43,8 @@ NVIpackager::document_NVIpkg(pkg = pkg,
                              readme = FALSE,
                              manual = "update",
                              scope = c("spaces", "line_breaks"))
+# filename <- "xxxx.R"
+# styler::style_file(path = file.path(pkg_path, "R", filename), scope = I(c("spaces")))
 
 # spelling::spell_check_package(vignettes = TRUE, use_wordlist = TRUE)
 

vignettes/NVI_vignette_style.css

@@ -0,0 +1,11 @@
+h1, h2, h3, h4 {
+  color: #1b314f; 
+  font-family: "Open Sans", "Helvetica Neue", Helvetica, Arial, sans-serif;
+}
+body {
+  color: #1b314f;
+  font-family: "source-serif-pro", "merriweather", serif;
+}
+thead {
+  font-family: "Open Sans", "Helvetica Neue", Helvetica, Arial, sans-serif;
+}